plotMotifLogo: plot sequence logo

In jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

plot sequence logo

Description

plot amino acid or DNA sequence logo

Usage

plotMotifLogo(
  pfm,
  motifName,
  p = rep(0.25, 4),
  font = "sans",
  fontface = "bold",
  colset = c("#00811B", "#2000C7", "#FFB32C", "#D00001"),
  xaxis = TRUE,
  yaxis = TRUE,
  xlab = "position",
  ylab = "bits",
  xlcex = 1.2,
  ylcex = 1.2,
  ncex = 1.2,
  ic.scale = TRUE,
  newpage = TRUE,
  margins = c(4.1, 4.1, 2.1, 0.1),
  draw = TRUE,
  ...
)

Arguments

pfm	a position frequency matrices
motifName	motif name
p	background possibility
font	font of logo
fontface	fontface of logo
colset	color setting for each logo letter
xaxis	draw x-axis or not. If a vector of character or numeric is provided, the function will try to plot the x-axis by setting the labels as the vectors.
yaxis	draw y-axis or not
xlab	x-label, do nothing if set xlab as NA
ylab	y-label, do nothing if set ylab as NA
xlcex	cex value for x-label
ylcex	cex value for y-label
ncex	cex value for motif name
ic.scale	logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height. It will also can be set as FALSE followed by a numeric vectors. The format is c(FALSE, scale). If it is FALSE followed by a number (eg c(FALSE, 100)), the y axis labels will be re-scaled by 100.
newpage	logical If TRUE, plot it in a new page.
margins	A numeric vector interpreted in the same way as par(mar) in base graphics.
draw	Vector (logical(1)). TRUE to plot. FALSE, return a gList
...	Not used.

Value

none

Examples

pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
pfm<-pcm2pfm(pcm)
rownames(pfm)<-c("A","C","G","T")
plotMotifLogo(pfm)

jianhong/motifStack documentation built on Jan. 31, 2024, 5:03 a.m.